Michael:
Okay, I see what you're saying. I guess my personal preference as far as setting it up, would be to test for whichever viewport the mouse is in when a hotkey is pressed to access those functions, and then apply the zoom or pan only to that particular viewport, and if the mouse isn't in a viewport nothing would happen.
That way a person can zoom or pan 1 viewport, but still retain an overall view from the other ports. Does that make sense? Anyway, that's my 2 cents.... :)

Paul